That's a reasonable question. There are a few, very limited experimental examples of positionally controlled chemical reactions. Regarding more general capabilities that may be available in the future, here's, for instance, an interesting and relevant peer-reviewed theoretical analysis:

http://www.molecularassembler.com/Papers/TarasovFeb2010.pdf

That link is from Freitas's website. You can also see the abstract in the publisher's site, but the full text seems to be paywalled:

http://www.aspbs.com/ctn/contents-ctn2010.htm#v7n1

https://www.ingentaconnect.com/content/asp/jctn/2010/00000007/00000002/art00002;jsessionid=132a35vdij2o1.x-ic-live-02